I could see an extra pair of speakers mounted in there. Make it a six speaker stereo system.
You could mount some LCD screens in there if thats your thing.
How about a fold up door, sort of like a mini glove box, could hide a number of things in there. Make them open up at the push of a button and have dual pistols mounted inside sort MIB style.
I personally like this idea. Get some clear acrylic cut to fit the location. Get someone to make you a vinyl sticker that you can overlay the acrlic with. My choice of design would be a vinyl that would completly cover the acrylic except for the scion logo in the center. Then mount your choice of lighting in the cubby and mount the acrylic over it. Now you have a light up logo in the rear. They even have small enough lighting now that you could install more then one color and have it set up so it changes coloring.
So many ideas for these areas. I can post more if your interested.